Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for NCOA2

Basic gene info.	Gene symbol	NCOA2
	Gene name	nuclear receptor coactivator 2
	Synonyms	GRIP1\|KAT13C\|NCoA-2\|SRC2\|TIF2\|bHLHe75
	Cytomap	UCSC genome browser: 8q13.3
	Genomic location	chr8 :71024266-71316020
	Type of gene	protein-coding
	RefGenes	NM_006540.2,
	Ensembl id	ENSG00000140396
	Description	class E basic helix-loop-helix protein 75glucocorticoid receptor-interacting protein-1hTIF2transcriptional intermediary factor 2
	Modification date	20141207
dbXrefs	MIM : 601993
	HGNC : HGNC
	Ensembl : ENSG00000140396
	HPRD : 09066
	Vega : OTTHUMG00000164671
Protein	UniProt: Q15596 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NCOA2
	BioGPS: 10499
	Gene Expression Atlas: ENSG00000140396
	The Human Protein Atlas: ENSG00000140396
Pathway	NCI Pathway Interaction Database: NCOA2
	KEGG: NCOA2
	REACTOME: NCOA2
	ConsensusPathDB
	Pathway Commons: NCOA2
Metabolism	MetaCyc: NCOA2
	HUMANCyc: NCOA2
Regulation	Ensembl's Regulation: ENSG00000140396
	miRBase: chr8 :71,024,266-71,316,020
	TargetScan: NM_006540
	cisRED: ENSG00000140396
Context	iHOP: NCOA2
	cancer metabolism search in PubMed: NCOA2
	UCL Cancer Institute: NCOA2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NCOA2 in cancer cell metabolism	1. Qin J, Lee H-J, Wu S-P, Lin S-C, Lanz RB, et al. (2014) Androgen deprivation–induced NCoA2 promotes metastatic and castration-resistant prostate cancer. The Journal of clinical investigation 124: 5013. go to article

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Phenotypic Information for NCOA2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: NCOA2
	Familial Cancer Database: NCOA2

* This gene is included in those cancer gene databases.

						.
Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	601993; gene.
Orphanet
Disease	KEGG Disease: NCOA2
	MedGen: NCOA2 (Human Medical Genetics with Condition)
	ClinVar: NCOA2
Phenotype	MGI: NCOA2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: NCOA2

Mutations for NCOA2

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	NCOA2	chr8	71077499	71077519	NCOA2	chr8	71061252	71061272
ovary	NCOA2	chr8	71156369	71156389	NCOA2	chr8	71152679	71152699
ovary	NCOA2	chr8	71267491	71267511	NCOA2	chr8	71268959	71268979
ovary	NCOA2	chr8	71281406	71281426	NCOA2	chr8	71295100	71295120
pancreas	NCOA2	chr8	71079954	71079974		chr8	77478156	77478176
pancreas	NCOA2	chr8	71081030	71081050	NCOA2	chr8	71081315	71081335

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NCOA2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
EF374064	KAT6A	1	75	8	41794774	41794848	NCOA2	75	476	8	71053441	71057084
AW979049	NCOA2	90	243	8	71218596	71218749	SLC35B4	241	456	7	133984283	133986549
BG260721	NCOA2	1	296	8	71261230	71261525	SLC7A1	281	418	13	30083551	30083688
AA829002	NCOA2	4	188	8	71218565	71218749	NCOA2	184	326	8	71218447	71218589
BG674032	NCOA2	1	155	8	71172635	71172788	MAP2K3	148	723	17	21213574	21214148
AA829004	NCOA2	4	188	8	71218565	71218749	NCOA2	184	330	8	71218447	71218593
DA677327	NCOA2	1	129	8	71315935	71316063	KLHL28	129	595	14	45414354	45415132
BG222207	HMGN3	7	105	6	79923102	79923200	NCOA2	106	257	8	71294826	71294977
BE009179	NCOA2	10	380	8	71110391	71110761	PTPRE	364	443	10	129789785	129789864
BF379189	AKAP13	1	235	15	85959552	85959789	NCOA2	227	362	8	71246232	71246367
BE149299	THSD7B	160	180	2	137875796	137875816	NCOA2	168	409	8	71218444	71218685
BF811949	NCOA2	23	315	8	71092000	71092293	NCOA2	310	464	8	71091671	71091825
BF088409	NCOA2	3	142	8	71246435	71246573	RHOB	141	436	2	20648632	20648927
AL706656	NCOA2	23	43	8	71290981	71291001	CAPZB	26	826	1	19672171	19672964

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	4			1			1		2		2			1	1
GAIN (# sample)	3			1			1		2		1			1	1
LOSS (# sample)	1										1

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=134)	Stat. for Synonymous SNVs (# total SNVs=34)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr8:71074996-71074996	p.A309V	3
chr8:71078928-71078928	p.R201R	3
chr8:71069190-71069190	p.P470P	2
chr8:71078966-71078966	p.E189*	2
chr8:71087031-71087031	p.G108D	2
chr8:71068807-71068807	p.G598V	2
chr8:71039182-71039182	p.R1261Q	2
chr8:71033539-71033539	p.R1461W	2
chr8:71069449-71069449	p.P384L	2
chr8:71068854-71068854	p.S582S	2

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3	4	1	29	2		5		4	1		13	9	2	1		13	22		14
# mutation	3	4	1	28	2		5		4	1		16	9	2	1		16	30		20
nonsynonymous SNV	3	2		23	1		3		2			15	8	2	1		13	22		13
synonymous SNV		2	1	5	1		2		2	1		1	1				3	8		7

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr8:71074996	p.A309V	3
chr8:71068967	p.P384L	2
chr8:71039179	p.L1206P	2
chr8:71037031	p.G545W	2
chr8:71039182	p.R1329L	2
chr8:71044133	p.P470P	2
chr8:71040732	p.R201R	2
chr8:71069449	p.R1088P	2
chr8:71069190	p.T1262N	2
chr8:71078928	p.R1261Q	2

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for NCOA2 in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for NCOA2

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


APOOL,ARFGEF1,ASXL2,CCNT1,CLOCK,DDI2,GTF2A1, LMBRD2,NCOA2,RAPGEF6,REST,RSC1A1,SERINC5,TMED10P1, UBR5,UHMK1,VCPIP1,VPS13B,YTHDF3,ZNF623,ZNF704	ARFGEF2,BIRC6,BPTF,CCNT1,CHD6,EP300,KDM5A, LATS1,LMTK2,MGA,MYSM1,NCOA2,PDPK1,RAPGEF6, REST,RSF1,SMCR8,UBR5,ZKSCAN1,ZKSCAN8,ZNF827

ARFGEF1,ASXL2,CCNT1,DDI2,EP300,FAM168A,GTF2A1, HIPK3,LATS1,LCOR,MYO9A,NCOA2,RC3H2,REL, REST,STRN,TAOK1,UBR5,VPS13B,ZNF623,ZNF827	ARHGEF12,ATXN7,BIRC6,CCDC93,EP300,FOXJ3,GBF1, GOLGB1,HEATR5B,KDM5A,LCOR,MARCH6,MGAT5,MTMR3, NCOA2,NCOA6,NF1,RALGAPB,SOS1,UBR4,ZFYVE26

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for NCOA2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2095163; -.
Organism-specific databases	PharmGKB	PA31471; -.
Organism-specific databases	CTD	10499; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01645	nuclear receptor coactivator 2	experimental	Genistein
DB02998	nuclear receptor coactivator 2	experimental	Methyltrienolone
DB06871	nuclear receptor coactivator 2	experimental	17-METHYL-17-ALPHA-DIHYDROEQUILENIN
DB06898	nuclear receptor coactivator 2	experimental	4-(2-amino-1-methyl-1H-imidazo[4,5-b]pyridin-6-yl)phenol
DB07080	nuclear receptor coactivator 2	experimental	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE
DB07086	nuclear receptor coactivator 2	experimental	4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-8-METHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07087	nuclear receptor coactivator 2	experimental	4-[(1S,2S,5S,9R)-5-(HYDROXYMETHYL)-8,9-DIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07195	nuclear receptor coactivator 2	experimental	4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-6,8,9-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB07678	nuclear receptor coactivator 2	experimental	(9ALPHA,13BETA,17BETA)-2-[(1Z)-BUT-1-EN-1-YL]ESTRA-1,3,5(10)-TRIENE-3,17-DIOL
DB07707	nuclear receptor coactivator 2	experimental	(9BETA,11ALPHA,13ALPHA,14BETA,17ALPHA)-11-(METHOXYMETHYL)ESTRA-1(10),2,4-TRIENE-3,17-DIOL
DB07708	nuclear receptor coactivator 2	experimental	3-CHLORO-2-(4-HYDROXYPHENYL)-2H-INDAZOL-5-OL
DB07712	nuclear receptor coactivator 2	experimental	3-ETHYL-2-(4-HYDROXYPHENYL)-2H-INDAZOL-5-OL
DB07863	nuclear receptor coactivator 2	experimental	2-chloro-5-nitro-N-phenylbenzamide
DB07932	nuclear receptor coactivator 2	experimental	dimethyl (1R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate
DB08047	nuclear receptor coactivator 2	experimental	4-[1-allyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol
DB08048	nuclear receptor coactivator 2	experimental	4-(6-HYDROXY-1H-INDAZOL-3-YL)BENZENE-1,3-DIOL
DB08175	nuclear receptor coactivator 2	experimental	(2E,4E)-11-METHOXY-3,7,11-TRIMETHYLDODECA-2,4-DIENOIC ACID
DB08320	nuclear receptor coactivator 2	experimental	DIETHYL (1R,2S,3R,4S)-5,6-BIS(4-HYDROXYPHENYL)-7-OXABICYCLO[2.2.1]HEPT-5-ENE-2,3-DICARBOXYLATE
DB08398	nuclear receptor coactivator 2	experimental	2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE
DB08402	nuclear receptor coactivator 2	experimental	2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID
DB08595	nuclear receptor coactivator 2	experimental	4-[(1S,2R,5S)-4,4,8-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL
DB08601	nuclear receptor coactivator 2	experimental	tributylstannanyl
DB08773	nuclear receptor coactivator 2	experimental	RALOXIFENE CORE

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Cross referenced IDs for NCOA2

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information